in other words, fabricate the flange on the backside of the door where needed?
The other day I did a lower door skin that I fabricated and on the other side I did just that...cut a chunk of the flange out, replaced a piece on the inners and welded a piece back to look like the flange. I also didn't cut it all the way at the bottom cause the metal was ok there so I didn't have to file it down or worry about it changing the gap to the rocker. Saved soo much time doing it that way. Good call.

Funny, I'm actually editing a video on the lower door skin and left out the footage of the repair of the flange being cut out on the other side but after this thread I will probably go back and insert it into the video.

Yep that is what I am saying, cut that rusted area out with a cut off disc. Run the cut straight down thru the folded lip of the skin but not the outside. Lift the fold a little so you can pull the cut piece out, and to clean the inside of the area for repair. That lip may even need to be completely cut out, cut it out by running a cut along the edge just on the inside of the fold.

Fab the new inner piece, weld it in then cut a small strip of metal to replace the piece of the folded lip of the skin.